[gmx-users] ligand-protein distance restraint

[Mark Abraham]

Pathumwadee Intharathep wrote:
> Dear gmx-users,
>  
> Do you know how to make distance restraint between ligand and protein in 
> gromacs?
> I have a chain of protein binds with 4 drugs in water-lipid box, the 
> topology put below..
> 
> ;       File 'top.top' was generated; Include forcefield parameters
> ;
> #include "/home/bio001/02_saow/gromacs_top/jit/top/ffgmx.itp"
> #include "/home/bio001/02_saow/gromacs_top/jit/popc.itp"

You can avoid the need to specify particular directories each time 
through careful use of the GMXLIB environment variable, or using 
"include = -I /some/dir" in your .mdp file. See 
http://wiki.gromacs.org/index.php/Include_File_Mechanism

You should also refrain from using ffgmx, as it's been deprecated for 
ages now.

> ; Include chain topologies
> #include "1add_H/0H_addH1.top"              ;protein atom 1-1615
> #include "disre.itp"                                      ; distance 
> restraint topology file
> #include "rimq1_top.itp"                              ;ligand topology 
> file atom 1-16
> ; Include water topology
> #include "/home/bio001/02_saow/gromacs_top/jit/top/flexspc.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> ; Include generic topology for ions
> #include "/home/bio001/02_saow/gromacs_top/jit/top/ions.itp"
> [ system ]
> ; Name
> Protein
> [ molecules ]
> ; Compound        #mols
> Protein_A             1
> RIM                      4
> POPC                  74
> SOL                   3763
> Cl                       8
> 
>  
> 
> ------------------------------------------
> 
> detailed in "disre.itp" file is
> [ distance_restraints ]
> 
>      195   1628   1   1     1   0.25 0.35 0.40 1.0
> 
>      195    563   1   1     1   0.25 0.35 0.40 1.0
> 
>      598   1644   1   1     1   0.25 0.35 0.40 1.0
> 
>      598    966   1   1     1   0.25 0.35 0.40 1.0
> 
>     1001   1660   1   1     1   0.25 0.35 0.40 1.0
> 
>     1001    369   1   1     1   0.25 0.35 0.40 1.0
> 
>     1404   1676   1   1     1   0.25 0.35 0.40 1.0
> 
>     1404    160   1   1     1   0.25 0.35 0.40 1.0
> 
> 
> The error occur after grompp run is..
> 
>  
> 
> “Fatal error: [ file "../disre.itp", line 2 ]:
> 
>              Atom index (1628) in distance_restraints out of bounds 
> (1-1615)”
> 
>  
> 
> It seems to be that the atoms from ligand (rimq1_top.itp) topology was 
> not known.
> 
> My question is 
> Q1: Where I should put “disre.itp” in topology file that it can 
> recognize the atom from both protein (0H_addH1.top) and ligand 
> (rimq1_top.itp) topology files.

Distance restraints may only be intra-molecular. Thus you will need to 
make a hybrid [molecule] section that includes your protein and all of 
its distance-restrained ligands and #include "disre.itp" at the end of 
that [molecule] section.

Mark